The latest executions bring to four the number of hangings since President Mokgweetsi Masisi was elected last October.
Moabi Seabelo Mabiletsa, 33, and his co-accused Matshidiso Tshid Boikanyo, 39, were hanged to death in the capital Gaborone, the prison services said in a statement.
The two were handed the death sentence for the murder of a taxi driver six years ago.
Botswana, which previously executed a man last month and another one in December, is the only country in southern Africa still regularly hanging convicts.
The death penalty has been legal in Botswana since its independence from Britain in 1966.
Nearly three-quarters of the world's 195 states have either abolished the punishment or not carried it out over the past decade, according to rights group Amnesty International.
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